X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=build.xml;h=e9006caf7e966c25b30b812efd46bb3e4dfdb148;hb=12f07d8817c2495feb46dc344de946f234313167;hp=be92845147837c44ee51a68fc72363f6f6afcd4b;hpb=893d172cea331f799692ce4ee93e9c080e644547;p=jalview.git

diff --git a/build.xml b/build.xml
index be92845..e9006ca 100755
--- a/build.xml
+++ b/build.xml
@@ -1,89 +1,862 @@
 <?xml version="1.0"?>
-<project name="jalviewX" default="build" basedir=".">
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<project name="jalviewX" default="usage" basedir=".">
+  <target name="help" depends="usage" />
+  <target name="usage">
+    <echo message="~~~Jalview Ant build.xml Usage~~~~" />
+    <echo message="Targets include:" />
+    <echo message="usage - default target, displays this message" />
+    <echo message="buildindices - generates JavaHelpSearch from the help files" />
+    <echo message="build - compiles all necessary files for Application" />
+    <echo message="makedist - compiles and places all necessary jar files into directory dist" />
+    <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
+    <echo message="              this needs a keystore and key. See docs/building.html for more information." />
+    <echo message="compileApplet - compiles all necessary files for Applet" />
+    <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
+    <echo message="See docs/building.html and the comments in build file for other targets." />
+    <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
+    <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
+  </target>
+
+
   <!-- utils is a class path to additional utilities needed for
-  building docs, jars and webstart stuff -->
+    building docs, jars and webstart stuff -->
+  <!--
+        Userdefined build property defaults
+
+        wsdl.server list (plus namespace mapping info ???)  - also want
+                ... to make this a dynamically generatable property
+        WebStart Location
+        Build location - provide a temporary root for speed
+        jarsigner keystore and info
+        Jakarta and axis classpath ?
+        Default argument for starting Jalview (if it exists).
+
+-->
 
   <target name="init">
+    <path id="axis.classpath">
+      <!-->
+      <fileset dir="/usr/local/axis/lib">
+        <include name="**/*.jar" />
+      </fileset>
+      <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
+        <include name="**/*.jar"/>
+        <include name="*.jar"/>
+      </fileset> -->
+      </path>
+  	
+    <!-- Jalview Version String displayed by application on startup and used to check for updates -->
+    <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
+  	
+    <property name="INSTALLATION" value="Source" />
+  	
+    <!-- 2.4 (VAMSAS)" -->
+    <!-- Include debugging information in javac true or false -->
+    <property name="javac.debug" value="true" />
+
+    <!-- JarSigner Key Store for Webstart Distribution -->
+    <property name="jalview.keystore" value="./keys/.keystore" />
+    <!-- Keystore Password -->
+    <property name="jalview.keystore.pass" value="alignmentisfun" />
+    <!-- Key Name -->
+    <property name="jalview.key" value="jalview" />
+    <!-- Key Password -->
+    <property name="jalview.key.pass" value="alignmentisfun" />
+
+    <!-- Don't change anything below here unless you know what you are doing! -->
+    <!-- Url path for WebStart in JNLP file -->
+    <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
+    <!-- Webstart Image - looked for in resources/images -->
+    <property name="WebStartImage" value="JalviewLogo_big.png"/>
+    <!-- J2SE version needed for webstart launch -->
+    <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
+    <property name="j2sev" value="1.7+"/>
+	<!-- Java Compilation settings - source and target javac version -->
+	<property name="javac.source" value="1.7"/>
+  	<property name="javac.target" value="1.7"/>
+  	  	
+    <!-- Permissions for running Java applets and applications. -->
+    <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
+    <property name="application.codebase" value="*.jalview.org" />
+    <!-- and allowing the applet to be deployed from any URL -->
+    <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
+    <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
+    <property name="applet.caller-codebase" value="${applet.codebase}" />
 
-    <property name="libDir" value="lib"/>
-    <property name="resourceDir" value="resources"/>
-    <property name="helpDir" value="help"/>
-    <property name="docDir" value="doc"/>
+    <!-- build directory configuration -->
+    <property name="libDir" value="lib" />
+    <property name="resourceDir" value="resources" />
+    <property name="helpDir" value="help" />
+    <property name="docDir" value="doc" />
     <property name="sourceDir" value="src" />
+    <property name="schemaDir" value="schemas" />
     <property name="outputDir" value="classes" />
+    <property name="packageDir" value="dist" />
     <property name="outputJar" value="jalview.jar" />
+    <!-- Jalview Applet JMol Jar Dependency -->
+    <property name="jmolJar" value="JmolApplet-14.2.14_2015.06.11.jar" />
+    <property name="varnaJar" value="VARNAv3-93.jar" />
+    <property name="jsoup" value="jsoup-1.8.1.jar" />
+    <property name="jsonSimple" value="json_simple-1.1.jar" />
+    <property name="javaJson" value="java-json.jar" />
+    <property name="jalviewLiteJar" value="jalviewApplet.jar" />
+	<property name="reportDir" value="test-reports" />
+	<property name="testDir" value="test" />
+	<property name="testOutputDir" value="tests" />
+    <!-- switch to indicate if we should obfuscate jalviewLite -->
+    <!-- <property name="donotobfuscate" value="true"/> -->
+    <!-- switch to exclude associations from generated jnlp files -->
+    <!-- <property name="nojnlpfileassocs" value="true"/> -->
 
+    <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
+    <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
+    <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
+    <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
+    <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
+    <property name="WSInterf" value="MsaWS" />
+    <property name="wsdl.Namespace" value="vamsas" />
+    <property name="wsdl.ClientNS" value="ext.vamsas" />
+    <!-- the class path for building the application -->
     <path id="build.classpath">
       <fileset dir="utils">
-        <include name="*.jar"/>
-        <include name="**/*.jar"/>
+        <include name="*.jar" />
+        <include name="**/*.jar" />
       </fileset>
       <fileset dir="${libDir}">
-        <include name="*.jar"/>      
-        <include name="**/*.jar"/>
+        <include name="*.jar" />
+        <include name="**/*.jar" />
       </fileset>
+      <fileset dir="${java.home}/lib">
+        <include name="plugin.jar"/>
+      </fileset>
+      <fileset dir="appletlib">
+        <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
+				-->
+        <include name="${jmolJar}" />
+        <include name="${varnaJar}" />
+      </fileset>
+
+    </path>
+    <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
+    <!-- The Location of the java 1.1.8 jdk -->
+    <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
+    <property name="java118.home" value="${java.home}" />
+    <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
+		-->
+    <!-- jre for 1.4 version -->
+    <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
+
+    <!-- the classpath for building the 1.1 applet -->
+    <path id="jalviewlite.deps">
+      <fileset dir="${java118.home}">
+        <include name="lib/classes.zip" />
+      </fileset>
+      <fileset dir="${java.home}/lib">
+        <include name="plugin.jar"/>
+      </fileset>
+      <pathelement location="appletlib/${jmolJar}" />
+      <pathelement location="lib/${varnaJar}" />
+      <pathelement location="lib/${jsoup}" />
+      <pathelement location="lib/${jsonSimple}" />
+      <pathelement location="lib/${javaJson}" />
+      
     </path>
+    <!-- default location for outputting javadoc -->
+    <property name="javadocDir" value="${packageDir}/javadoc"/>
+  </target>
+
 
+  <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
+  <target name="buildPropertiesFile" depends="init">
+    <tstamp prefix="build">
+      <format property="date" pattern="dd MMMM yyyy" />
+    </tstamp>
+    <exec executable="/usr/bin/git" outputproperty="git.commit"  failifexecutionfails="false">
+      <arg value="rev-parse"/>
+      <arg value="--short"/>
+      <arg value="HEAD"/>
+    </exec>
+    <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
+      <arg value="rev-parse"/>
+      <arg value="--abbrev-ref"/>
+      <arg value="HEAD"/>
+    </exec>
+    <properties file="${outputDir}/.build_properties">
+      <header>
+          ---Jalview Build Details---
+        </header>    	
+      <property name="VERSION" value="${JALVIEW_VERSION}" />
+      <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
+      <property name="BUILD_DATE" value="${build.date}" />
+    </properties>
   </target>
 
+
   <target name="clean" depends="init">
-        <!-- not efficient yet. -->
-    <delete dir="${outputDir}"/>
+    <!-- not efficient yet. -->
+    <delete dir="${outputDir}" includes="*,**/*"/>
   </target>
 
   <target name="distclean" depends="init, clean">
-    
-    <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
+
+    <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
     <delete>
       <fileset dir=".">
-        <include name="${outputJar}"/>
-        <include name="#*#"/>
-        <include name="#*.*#"/>
-        <include name="**/#*#"/>
-        <include name="**/#*.*#"/>
-        <include name="*~"/>
-        <include name="*.*~"/>
-        <include name="**/*~"/>
-        <include name="**/*.*~"/>
+        <include name="${outputJar}" />
+        <include name="#*#" />
+        <include name="#*.*#" />
+        <include name="**/#*#" />
+        <include name="**/#*.*#" />
+        <include name="*~" />
+        <include name="*.*~" />
+        <include name="**/*~" />
+        <include name="**/*.*~" />
       </fileset>
     </delete>
   </target>
-  
+
   <target name="prepare" depends="init">
-    <mkdir dir="${outputDir}"/>
+    <mkdir dir="${outputDir}" />
     <copy todir="${outputDir}">
       <fileset dir=".">
-
-        <include name="${docDir}/**/*.*"/>
-        <include name="${helpDir}/**/*.*"/>
-        <include name="${libDir}/*.*"/>
+        <include name="${docDir}/**/*.*" />
+        <include name="${helpDir}/**/*.*" />
+        <include name="${libDir}/*.jar" />
       </fileset>
       <fileset dir="${resourceDir}">
-        <include name="**/*.*"/>
+        <include name="**/*.*" />
       </fileset>
     </copy>
   </target>
 
   <target name="build" depends="prepare">
-            <!-- not efficient yet. -->
-     <javac srcdir="${sourceDir}" destdir="${outputDir}"
-        classpathref="build.classpath" />
+    <!-- not efficient yet. -->
+    <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
+      <exclude name="jalview/*applet*" />
+      <exclude name="jalview/appletgui/**" />
+      <exclude name="com/stevesoft/**" />
+    </javac>
+  </target>
+  
+  
+  <target name="testclean" depends="init">
+    <delete dir="${testOutputDir}" includes="*,**/*"/>
+  </target>
+  
+  <target name="prepareTests" depends="init">
+	<mkdir dir="${testOutputDir}" />
+	<copy todir="${testOutputDir}">
+		<fileset dir=".">
+			<include name="${docDir}/**/*.*" />
+			<include name="${helpDir}/**/*.*" />
+			<include name="${libDir}/*.jar" />
+		</fileset>
+		<fileset dir="${resourceDir}">
+			<include name="**/*.*" />
+		</fileset>
+	</copy>
+  </target>  
+  
+  <target name="buildTests" depends="prepareTests">
+	<javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${testOutputDir}"
+		debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >		
+	</javac>
+	<javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}"
+		debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
+	</javac>
+  </target>
+  
+  <taskdef name="testng" classname="org.testng.TestNGAntTask" >	    
+	<classpath location="utils/testnglibs/testng.jar" />
+  </taskdef>
+  
+  <target name="testng" depends="buildTests">
+	<testng classpathref="build.classpath" outputDir="${reportDir}"
+		haltOnFailure="false">
+		<classpath location="${testOutputDir}" />
+		<xmlfileset dir="utils" includes="jalview_testng.xml" />
+	</testng>
+  </target>
+  
+  <target name="buildindices" depends="init, prepare" unless="help.uptodate">
+    <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
+      <arg line="html" />
+    </java>
   </target>
+
+  <target name="makefulldist" depends="makedist">
+    <copy todir="${packageDir}">
+      <fileset dir="${resourceDir}/images">
+        <include name="${WebStartImage}"/>
+      </fileset>
+    </copy>
+
+    <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
+
+    <!-- create a dummy jar which will eventually contain the jnlp template -->
+    <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
+      <fileset dir="${packageDir}">
+        <include name="jalview.jar" />
+      </fileset>
+    </jar>
+
+    <mkdir dir="${packageDir}/JNLP-INF"/>
+    <antcall target="writejnlpf">
+      <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
+      <param name="inih" value="*" />
+      <param name="maxh" value="*"/>
+    </antcall>
+
+    <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
+      <fileset dir="${packageDir}">
+        <include name="JNLP-INF"/>
+      </fileset>
+    </jar>
+
+    <antcall target="writejnlpf">
+      <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
+      <param name="inih" value="10M" />
+      <param name="maxh" value="256M"/>
+    </antcall>
+
+    <antcall target="writejnlpf">
+      <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
+      <param name="inih" value="128M" />
+      <param name="maxh" value="512M"/>
+    </antcall>
+
+    <antcall target="writejnlpf">
+      <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
+      <param name="inih" value="256M" />
+      <param name="maxh" value="1024M"/>
+    </antcall>
+
+    <!-- finally, need to postprocess to add in associations at end of 'information' element 
+			
+			<xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
+		
+		</xslt>
+			
+			
+			-->
+    <!--
+				<association mime-type="application-x/ext-file" extensions="fa"/>
+        <association mime-type="application-x/ext-file" extensions="fasta"/>
+        <association mime-type="application-x/ext-file" extensions="mfa"/>
+        <association mime-type="application-x/ext-file" extensions="fastq"/>
+        <association mime-type="application-x/ext-file" extensions="blc"/>
+        <association mime-type="application-x/ext-file" extensions="msf"/>
+        <association mime-type="application-x/ext-file" extensions="pfam"/>
+        <association mime-type="application-x/ext-file" extensions="aln"/>
+        <association mime-type="application-x/ext-file" extensions="pir"/>
+        <association mime-type="application-x/ext-file" extensions="amsa"/>
+        <association mime-type="application-x/ext-file" extensions="stk"/>
+        <association mime-type="application-x/ext-file" extensions="jar"/>-->
+    <!-- and sign the jars -->
+    <!-- the default keystore details might need to be edited here -->
+    <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
+      <fileset dir="${packageDir}">
+        <include name="*.jar" />
+      </fileset>
+    </signjar>
+  </target>
+
   <target name="runenv" depends="init">
-      <path id="run.classpath">
-        <pathelement location="${outputDir}"/>
-        <fileset dir="${outputDir}">
-        <include name="${libDir}/*.jar"/>
+    <path id="run.classpath">
+      <pathelement location="${outputDir}" />
+      <fileset dir="${outputDir}">
+        <include name="${libDir}/*.jar" />
       </fileset>
     </path>
-    <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
-    
+    <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
+
     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
-    </echo>
-</target>
-  
+      </echo>
+  </target>
+
+  <target name="-generatejnlpf">
+    <presetdef name="jnlpf">
+      <jnlp codebase="${WebStartLocation}">
+        <information>
+          <title>Jalview</title>
+          <vendor>The Barton Group</vendor>
+          <homepage href="http://www.jalview.org" />
+          <description>Jalview Multiple Alignment Editor</description>
+          <description kind="short">Jalview</description>
+          <icon href="${WebStartImage}" />
+          <offline_allowed />
+        </information>
+        <resources>
+          <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
+          <fileset dir="${packageDir}">
+            <include name="jalview.jar" />
+          </fileset>
+          <fileset dir="${packageDir}">
+            <include name="*.jar" />
+            <include name="*_*.jar" />
+            <exclude name="jalview.jar" />
+          	<exclude name="*jnilib.jar"/>
+          </fileset>
+      	</resources>
+        <resources os="Mac OS X">
+          <property name="jalview.version" value="${JALVIEW_VERSION}" />
+        	<fileset dir="${packageDir}">
+        		<include name="*quaqua*.jnilib.jar"/>
+        	</fileset>
+        </resources>
+      	
+        <application_desc main_class="jalview.bin.Jalview">
+        </application_desc>
+        <security>
+          <all_permissions />
+        </security>
+      </jnlp>
+    </presetdef>
+
+    <jnlpf toFile="${jnlpFile}"/>
+
+  </target>
 
-  <target name="package" depends="init, build">
-    
+  <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
+    <echo message="Not adding JNLP File Associations"/>
   </target>
+
+  <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
+    <replace file="${jnlpFile}">
+      <replacetoken>
+        <![CDATA[</information>]]></replacetoken>
+      <replacevalue>
+        <![CDATA[
+          <association mime-type="application-x/ext-file" extensions="fa" />
+        <association mime-type="application-x/ext-file" extensions="fasta" />
+        <association mime-type="application-x/ext-file" extensions="mfa" />
+        <association mime-type="application-x/ext-file" extensions="fastq" />
+        <association mime-type="application-x/ext-file" extensions="blc" />
+        <association mime-type="application-x/ext-file" extensions="msf" />
+        <association mime-type="application-x/ext-file" extensions="pfam" />
+        <association mime-type="application-x/ext-file" extensions="aln"/>
+        <association mime-type="application-x/ext-file" extensions="pir"/>
+        <association mime-type="application-x/ext-file" extensions="amsa"/>
+        <association mime-type="application-x/ext-file" extensions="stk"/>
+        <association mime-type="application-x/ext-file" extensions="jvp"/>
+      </information>]]></replacevalue>
+  </replace>
+  <echo message="Added file associations to JNLP file"/>
+</target>
+<target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
+</target>
+
+<target name="buildextclients" depends="init">
+  <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
+  <condition property="dontextbuild">
+    <equals arg1="n" arg2="${doextbuild.response}" />
+  </condition>
+  <condition property="dontextbuild">
+    <equals arg1="N" arg2="${doextbuild.response}" />
+  </condition>
+  <fail if="dontextbuild">
+        Build External Client Code process aborted by user. Jalview source is unchanged.
+      </fail>
+  <!-- Currently, this doesn't happen automatically.
+     1. Run WSDL2Java as below, which generates an ext.vamsas +
+     vamsas.<datapackages> fileset.
+     2. refactor ext.vamsas.SpecificserviceWS* to
+     ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
+     3. Update the jalview.ws.*WServices classes to reflect the
+     interface type, and all locations of this wsdl type that Jalview
+     might be using.
+
+-->
+  <path id="axisbuild">
+    <path refid="build.classpath" />
+  </path>
+  <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
+  <move todir="./bak">
+    <fileset dir="${sourceDir}" id="client">
+      <include name="${wsdl.ClientNS}/*.*" />
+    </fileset>
+  </move>
+
+  <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
+    <mappingSet>
+      <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
+      <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
+    </mappingSet>
+  </axis-wsdl2java>
+</target>
+
+<target name="makedist" depends="build, buildPropertiesFile, buildindices">
+  <!-- make the package jar if not already existing -->
+  <mkdir dir="${packageDir}" />
+  <!-- clean dir if it already existed -->
+  <delete>
+    <fileset dir="${packageDir}">
+      <include name="*.jar"/>
+    </fileset>
+  </delete>
+  <jar destfile="${packageDir}/${outputJar}" index="true">
+    <manifest>
+      <attribute name="Main-Class" value="jalview.bin.Jalview" />
+      <attribute name="Permissions" value="all-permissions" />
+      <attribute name="Application-Name" value="Jalview Desktop" />
+      <attribute name="Codebase" value="${application.codebase}" />
+    </manifest>
+    <fileset dir="${outputDir}/">
+      <exclude name="cache*/**" />
+      <exclude name="*.jar" />
+      <exclude name="*.jar.*" />
+      <exclude name="**/*.jar" />
+      <exclude name="**/*.jar.*" />
+    </fileset>
+  </jar>
+
+  <copy toDir="${packageDir}" flatten="true">
+    <fileset dir="${outputDir}">
+      <include name="*.jar" />
+      <include name="**/*.jar" />
+    </fileset>
+  </copy>
+</target>
+
+
+<!-- jalopy code reformatter -->
+<target name="sourcescrub" depends="init,build">
+  <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
+    <fileset dir="${sourceDir}">
+      <include name="*.java" />
+      <include name="**/*.java" />
+      <include name="**/**/*.java" />
+    </fileset>
+  </jalopy>
+</target>
+
+
+
+<!-- Compile, package and obfuscate Jalview Applet -->
+<target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
+
+<target name="compileApplet" depends="init,clean">
+  <mkdir dir="${outputDir}" />
+  <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
+			classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
+			excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
+</target>
+
+<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
+  <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
+  <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
+  <copy todir="${outputDir}/lang">
+    <fileset dir="${resourceDir}/lang">
+      <include name="**.*"/>
+    </fileset>
+  </copy>
+  <jar destfile="in.jar" index="true">
+    <manifest>
+      <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
+      <attribute name="Application-Name" value="JalviewLite" />
+      <attribute name="Codebase" value="${applet.codebase}" />
+    </manifest>
+    <fileset dir="${outputDir}">
+      <include name="com/**" />
+      <include name="MCview/**" />
+      <include name="jalview/**" />
+      <include name=".build_properties" />
+      <include name="images/idwidth.gif" />
+      <include name="images/link.gif" />
+      <include name="lang/**" />
+    </fileset>
+  </jar>
+</target>
+<target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
+</target>
+<target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
+  <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
+  <delete file="in.jar" />
+</target>
+<target name="-obfuscatereally" unless="donotobfuscate">
+
+  <path id="obfuscateDeps.path">
+    <pathelement location="${applet.jre.tools}" />
+    <pathelement location="appletlib/${jmolJar}" />
+    <pathelement location="appletlib/${jsonSimple}" />
+    <pathelement location="appletlib/${javaJson}" />
+  </path>
+  <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+
+  <proguard>
+    <injar file="in.jar" />
+    <outjar file="${jalviewLiteJar}" />
+    <libraryjar refid="obfuscateDeps.path" />
+    <dontwarn/>
+    <keep access="public" type="class" name="jalview.bin.JalviewLite">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+    <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+    <!--      -libraryjars "${obfuscateDeps}"
+      -injars      in.jar
+      -outjars     jalviewApplet.jar
+      -keep public class jalview.bin.JalviewLite
+       { public * ; } -->
+  </proguard>
+  <delete file="in.jar" />
+</target>
+
+<target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
+  <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
+  <delete>
+    <fileset dir="${sourceDir}/jalview/schemabinding/version2">
+      <include name="*.java" />
+      <include name="descriptors/*.java" />
+    </fileset>
+  </delete>
+  <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
+  <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
+  <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
+  <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
+  <!-- 
+		now build the jalview.binding package with the old schema set
+		-->
+  <delete>
+    <fileset dir="${sourceDir}/jalview/binding/">
+      <include name="**" />
+    </fileset>
+  </delete>
+  <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+  <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+  <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+</target>
+<target name="sourcedist" description="create jalview source distribution" depends="init">
+  <delete file="${source.dist.name}" />
+  <tar destfile="${source.dist.name}" compression="gzip">
+    <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
+      <include name="LICENSE" />
+      <include name="README" />
+      <include name="build.xml" />
+      <include name="jalview-jalopy.xml" />
+      <include name="JalviewApplet.jpx" />
+      <include name="JalviewX.jpx" />
+      <include name="nbbuild.xml"/>
+      <include name="nbproject/genfiles.properties"/>
+      <include name="nbproject/project.properties"/>
+      <include name="nbproject/project.xml"/>
+      <include name="${sourceDir}/*.java" />
+      <include name="${sourceDir}/**/*.java" />
+      <include name="${sourceDir}/**/*.cdr" />
+      <include name="${libDir}/**/*" />
+      <include name="${resourceDir}/**/*" />
+      <include name="${helpDir}/**/*" />
+      <include name="appletlib/${jmolJar}" />
+      <exclude name="**/*locales" />
+      <exclude name="*locales/**" />
+      <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
+      <exclude name="utils/InstallAnywhere/**Build*/**" />
+      <exclude name="utils/InstallAnywhere/**Build*/**" />
+      <exclude name="utils/InstallAnywhere/**locale*" />
+      <exclude name="utils/InstallAnywhere/**locale*/**" />
+      <include name="${schemaDir}/**/*" />
+      <include name="utils/**/*" />
+      <include name="${docDir}/**/*" />
+      <include name="examples/**/*" />
+    </tarfileset>
+  </tar>
+</target>
+<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
+  <copy todir="${packageDir}/examples">
+    <fileset dir="examples">
+      <include name="**/*"/>
+      <include name="javascript/*"/>
+      <include name="jmol/*"/>
+    </fileset>
+    <fileset dir=".">
+      <include name="${jalviewLiteJar}" />
+    </fileset>
+    <fileset dir="appletlib">
+      <include name="**/*"/>
+    </fileset>
+  </copy>
+  <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
+  <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}"/>
+  <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}"/>
+  <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
+    <manifest>
+      <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
+      <!--          <attribute name="Permissions" value="sandbox" /> -->
+      <!--<attribute name="Trusted-Lib" value="true" /> -->
+      <attribute name="Codebase" value="${applet.codebase}"/>
+      <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
+    </manifest>
+  </jar>
+  <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+    <fileset dir="${packageDir}/examples">
+      <include name="*.jar" />
+    </fileset>
+  </signjar>
+  <presetdef name="ap_applet.jar">
+    <!-- build a signed applet with 'all-permissions' - 
+			  Needs 'param name="permissions' value="all-permissions"' in applet tag
+			  JalviewLite+JmolApplet linked sequence/structure fails
+			  Mixed code warnings are raised
+			  -->
+    <jar update="true" index="true">
+      <manifest>
+        <attribute name="Application-Name" value="JalviewLite" />
+        <attribute name="Permissions" value="all-permissions" />
+        <attribute name="Codebase" value="${applet.codebase}" />
+        <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
+        <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
+      </manifest>
+    </jar>
+  </presetdef>
+  <presetdef name="applet.jar">
+    <!-- build signed applet with sandbox permissions -
+			  Needs 'param name="permissions' value="sandbox"' in applet tag
+			 Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag 
+			-->
+
+    <jar update="true" index="true">
+      <manifest>
+        <attribute name="Application-Name" value="JalviewLite" />
+        <attribute name="Permissions" value="sandbox" />
+        <attribute name="Codebase" value="${applet.codebase}" />
+        <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
+        <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
+      </manifest>
+    </jar>
+  </presetdef>
+  <presetdef name="tl_applet.jar">
+    <!-- build signed applet with trusted library/trusted permissions -
+			        Needs 'param name="permissions' value="all-permissions"' in applet tag
+			       j1.7_45:
+			       No mixed code warnings raised 
+			       Jmol/JalviewLite sequence/structure example doesn't link structures
+			       Raises dialog asking user to allow page to control applet via LiveConnect javascript
+			       
+			      -->
+
+    <jar update="true" index="true">
+      <manifest>
+        <attribute name="Application-Name" value="JalviewLite" />
+        <attribute name="Permissions" value="all-permissions" />
+        <attribute name="Codebase" value="${applet.codebase}" />
+        <attribute name="Trusted-Only" value="true" />
+        <attribute name="Trusted-Library" value="true" />
+      </manifest>
+    </jar>
+  </presetdef>
+  <presetdef name="to_applet.jar">
+    <!-- not fully test variant (yet) -->
+    <jar update="true" index="true">
+      <manifest>
+        <attribute name="Application-Name" value="JalviewLite" />
+        <attribute name="Permissions" value="all-permissions" />
+        <attribute name="Codebase" value="${applet.codebase}" />
+        <attribute name="Trusted-Only" value="true" />
+      </manifest>
+    </jar>
+  </presetdef>
+  <!-- create differently privileged artefacts -->
+  <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
+  <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true"/>
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true"/>
+  <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
+  <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}"/>
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}"/>
+  <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
+  <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
+  <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
+  <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
+  <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
+  <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
+  <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
+  <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
+  <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
+  <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
+  <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
+  <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
+  <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
+  <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
+  <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
+  <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
+  <!-- finally, create manifest for original jars -->
+  <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
+  <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
+  <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
+  <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
+
+  <!-- todo - write examples/downloads for alternate versions of the applet -->
+  <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+
+    <fileset dir="${packageDir}/examples">
+      <exclude name="u_*.jar"/>
+      <include name="${jalviewLiteJar}" />
+      <include name="${jmolJar}" />
+      <include name="${javaJson}" />
+      <include name="${jsonSimple}" />
+      <include name="to_${jalviewLiteJar}" />
+      <include name="to_${jmolJar}" />
+      <include name="to_${javaJson}" />
+      <include name="to_${jsonSimple}" />
+      <include name="tl_${jalviewLiteJar}" />
+      <include name="tl_${jmolJar}" />
+      <include name="tl_${javaJson}" />
+      <include name="tl_${jsonSimple}" />
+      <include name="ap_${jalviewLiteJar}" />
+      <include name="ap_${jmolJar}" />
+      <include name="ap_${javaJson}" />
+      <include name="ap_${jsonSimple}" />
+    </fileset>
+  </signjar>
+  <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
+  <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+	<!-- finally, replace any launchApp servlet tags with a version specification -->
+	<replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
+		<replacetoken><![CDATA[http://www.jalview.org/services/launchApp"]]></replacetoken>
+		<fileset dir="${packageDir}/examples">
+			<include name="**/*.html"/>
+		</fileset>
+	</replace>
+	<replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
+		<replacetoken><![CDATA[http://www.jalview.org/services/launchApp']]></replacetoken>
+		<fileset dir="${packageDir}/examples">
+			<include name="**/*.html"/>
+		</fileset>
+	</replace>
+
+</target>
+<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
+  <javadoc destdir="${javadocDir}">
+    <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
+    </packageset>
+  </javadoc>
+</target>
 </project>